Caenorhabditis-HSE-Helitrons

This repository is a series of HSE-Helitron overlap analyses created by bvtsu for Garrigues et al., 2019. This HPC pipeline is controlled by bash commands to take a list of UCSC Genome Browser database-specific genome names (e.g. ce11 for Caenorhabditis elegans via UCSC) and uses them to create unique Torque jobs and run scripts and pre-built software contained in the src/ directory.

Published work with UCSC genomes suggest that this high % of HSEs in helitrons (red slice) is specific to Caenorhabditis.

In progress/planned

1. Refining python code to typehint and proper PEP8 style
2. Adding comment blocks to annotate code
3. Adding ETE3 pie chart analyses
4. Wormbase, Caenorhabditis Genome Project

Installing/Prerequisites

1. Install miniconda
2. Install RepeatMasker via conda (Optional: These genomes already have well-curated rmsk files associated with these databases)

   conda config --add channels bioconda
   conda install -c bioconda repeatmasker
   

3. twoBitToFa (Tool specifically for UCSC Genome Browser genomes)

   wget -P ~/ http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/twoBitToFa
   

   • Alternatively:

   conda install --yes -c bioconda ucsc-twobittofa
   

4. python 3.9 (not tested with other versions)

   conda install --yes python=3.9
   

5. other dependencies via conda

   conda install --yes pandas numpy
   

Usage

HPC usage will be demonstrated using a copy of the tests/integration planfile entries as an example.

1. Loop through planfile (.txt) of genome names to run again pipeline

   ./ucsc_process_helitrons.sh -i '/Path/to/repo/planfile_rmsk_sample.txt' -o '/Path/to/outfolder'
   

2. Make summaries -> Path/to/outfolder/HSE_in_out_summary.txt

   python summary.py -genomes '/Path/to/repo/planfile_rmsk_sample.txt' -o '/Path/to/outfolder'
   

Testing

Local usage will be demonstrated using the tests/integration planfile

1. Loop through planfile (.txt) of genome names to run again pipeline

   ./ucsc_process_helitrons_local.sh -i '/Path/to/repo/Caenorhabditis-HSE-Helitrons/tests/integration/planfile_rmsk_subset.txt' -o '/Path/to/repo/Caenorhabditis-HSE-Helitrons/tests/integration'
   

2. Make summaries -> tests/integration/HSE_in_out_summary.txt

   python summary.py -genomes '/Path/to/repo/Caenorhabditis-HSE-Helitrons/tests/integration/planfile_rmsk_subset.txt' -o '/Path/to/repo/Caenorhabditis-HSE-Helitrons/tests/integration'
   

Functional testing was done using HPC resources.